Investigation Title Circadian Transcriptome of the Chicken Pineal In Vitro Comment[Submitted Name] Circadian Transcriptome of the Chicken Pineal In Vitro Experimental Design transcription profiling by array Experimental Design Term Source REF EFO Comment[AEMIAMESCORE] 3 Comment[SecondaryAccession] Comment[SecondaryAccession] GSE5292 Comment[ArrayExpressReleaseDate] 2008-07-04 Comment[Publication DOI] 10.1186/1471-2164-9-206 Comment[ArrayExpressAccession] E-GEOD-5292 Comment[MAGETAB TimeStamp_Version] 2010-10-16 13:38:14 Last Changed Rev: 14677 Experimental Factor Name GENDER STRAIN DEVELOPMENTAL AGE Experimental Factor Type Gender Strain Developmental Age Experimental Factor Term Source REF Person Last Name Karaganis Kumar Beremand Bailey Beremand Cassone Thomas Person First Name Stephen Vinod Phillip Michael Phillip Vincent Terry Person Mid Initials P D. J D M L Person Email beremand@mail.bio.tamu.edu Person Phone 979-845-0663 Person Fax 979-847-8805 Person Address Biology, Texas A&M University, , College Station, TX, USA Person Affiliation Texas A&M University Person Roles submitter Person Roles Term Source REF The MGED Ontology Quality Control Type Quality Control Term Source REF Replicate Type Replicate Term Source REF Normalization Type Normalization Term Source REF Date of Experiment Public Release Date 2008-07-04 PubMed ID 18454867 Publication DOI 18454867 Publication Author List Karaganis SP, Kumar V, Beremand PD, Bailey MJ, Thomas TL, Cassone VM Publication Title Circadian genomics of the chick pineal gland in vitro. Publication Status journal_article Publication Status Term Source REF The MGED Ontology Experiment Description Chick pinealocytes exhibit all the characteristics of a complete circadian system, comprising photoreceptive inputs, molecular clockworks and an easily measured rhythmic output, melatonin biosynthesis. We used microarray analysis to investigate the expression of approximately 8000 genes within cultured pinealocytes subjected to both LD and DD cycles. We report that a reduced subset of genes were rhythmically expressed in vitro compared to those previously published in vivo, and that gene expression rhythms were lower in amplitude, although the functional distribution of the rhythmic transcriptome was largely similar. We also investigated the effects of 6-hour pulses of light or of norepinephrine on gene expression in free-running cultures during both subjective day and night. As expected, both light and norepinephrine inhibited melatonin production; however, the two treatments differentially up- or down-regulated specific sets of genes in a fashion that was dependent upon time of day. Our combined approach of utilizing a time of day study and a light/NE pulse microarray experiment allowed us to identify novel genes linking clock input to clock function within the pineal. We identified approximately 30 rhythmic, light-responsive, NE-insensitive genes with no previously known clock function, which may play a role in circadian regulation of the pineal. These are candidates for future functional genomics experiments to elucidate their potential role in pineal physiology. Keywords: circadian; avian; pineal; light; norepinephrine Microarray analysis was performed on pineal samples subjected to one of four experimental groups: cultures placed within a 12-hour light:12-hour dark cycle (LD); cultures placed in continuous darkness (DD); cultures subjected to a 6-hour light pulse beginning at either CT0 or CT12 (i.e., zero or 12 hours after the beginning of subjective day) or that received no light pulse; and cultures subjected to 6 hours of NE treatment beginning at either CT0 or CT12 or that received similarly administered vehicle. For LD and DD groups, time-course sampling was performed such that 6 samples were collected over the course of a day at 4-hour intervals. For the light pulse and NE administration groups, 2 samples were collected over the course of a day, either at CT6 or CT18 (i.e., 6 or 18 hours after the beginning of subjective day). Four biological replicates and two technical replicates (for each biological repeat) were performed for each sample. For the LD and DD groups, time-points ZT18 and CT18 served as the control reference for the time-course analysis. For the light pulse experiment, cultures that did not receive light served as the control. For the NE administration experiment, cultures that received vehicle served as the control. Dye swaps for performed for experimental samples from the light pulse and NE administration experiments. Protocol Name P-GSE5292-6 P-GSE5292-7 P-GSE5292-5 P-GSE5292-2 P-GSE5292-4 P-GSE5292-3 P-GSE5292-1 Protocol Type feature_extraction feature_extraction feature_extraction bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation Protocol Description GenePixPro was used to generate a .gpr file, which was analyzed using GeneSpring software. Data were then subjected to LOWESS normalization, and each time-point was reported as the normalized ratio of Cy5 to Cy3 intensity. GenePixPro was used to generate a .gpr file, which was analyzed using GeneSpring software. Data were then subjected to LOWESS and dye-swap normalizations, and each time-point was reported as the normalized ratio of Cy3 to Cy5 intensity. GenePixPro was used to generate a .gpr file, which was analyzed using GeneSpring software. Data were then subjected to LOWESS normalization, and each time-point was reported as the normalized ratio of Cy5 to Cy3 intensity. ID_REF =
VALUE = Natural logarithm of ratio of cy5 to cy3 ID_REF =
VALUE = Natural logarithm of ratio of cy3 to cy5 ID_REF =
VALUE = Pineal Culture LD ZT6 Replicate 1 ID_REF =
VALUE = Natural log of ratio of Cy5 to Cy3 Protocol Parameters Protocol Hardware Protocol Software Protocol Contact Protocol Term Source REF The MGED Ontology The MGED Ontology The MGED Ontology The MGED Ontology The MGED Ontology The MGED Ontology The MGED Ontology SDRF File E-GEOD-5292.sdrf.txt Term Source Name The MGED Ontology ArrayExpress EFO The MGED Ontology Term Source File http://mged.sourceforge.net/ontologies/MGEDontology.php http://www.ebi.ac.uk/arrayexpress http://www.ebi.ac.uk/efo/ http://mged.sourceforge.net/ontologies/MGEDontology.php Term Source Version